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18
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1 hmmpfam - search one or more sequences against HMM database
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2 HMMER 2.3.2 (Oct 2003)
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3 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
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4 Freely distributed under the GNU General Public License (GPL)
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5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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6 HMM file: myhmms
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7 Sequence file: test.fa
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8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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9
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10 Query sequence: pkinase_full
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11 Accession: [none]
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12 Description: Dario rerio
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13
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14 Scores for sequence family classification (score includes all domains):
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15 Model Description Score E-value N
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16 -------- ----------- ----- ------- ---
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17 pkinase Protein kinase domain 266.6 3.3e-80 1
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18 pkinase Protein kinase domain 265.4 7.6e-80 1
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19 rrm -42.5 2.5 1
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20 rrm -8.7 3.7 1
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21 fn3 Fibronectin type III domain -45.8 3.7 1
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22 fn3 Fibronectin type III domain -9.0 3.8 1
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23
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24 Parsed for domains:
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25 Model Domain seq-f seq-t hmm-f hmm-t score E-value
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26 -------- ------- ----- ----- ----- ----- ----- -------
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27 rrm 1/1 169 180 .. 66 77 .] -8.7 3.7
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28 fn3 1/1 197 200 .. 81 84 .] -9.0 3.8
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29 rrm 1/1 256 319 .. 1 77 [] -42.5 2.5
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30 pkinase 1/1 258 540 .. 1 294 [] 266.6 3.3e-80
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31 pkinase 1/1 258 537 .. 1 289 [. 265.4 7.6e-80
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32 fn3 1/1 434 506 .. 1 84 [] -45.8 3.7
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33
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34 Alignments of top-scoring domains:
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35 rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
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36 *->nGkelggrklrv<-*
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37 n++ ++l v
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38 pkinase_fu 169 NKQDPHQHRLSV 180
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39
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40 fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
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41 CS CCCC
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42 *->GpeS<-*
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43 G eS
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44 pkinase_fu 197 GGES 200
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45
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46 rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
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47 *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
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48 +N++ +d+ e + F+ + +++ +
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49 pkinase_fu 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285
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50
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51 kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
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52 + V++ +ee+ ++ ++++ + l++ +
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53 pkinase_fu 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319
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54
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55 pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80
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56 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
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57 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
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58 pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
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59
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60 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
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61 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
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62 pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
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63
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64 ng........................gplsekeakkialQilrGleYLHs
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65 + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL +
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66 pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402
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67
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68 ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
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69 +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p +
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70 pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451
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71
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72 mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
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73 +m+PE ++++ y+s++DvW++Gv+L+E++++g
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74 pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483
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75
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76 dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
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77 ++P+++ + ee+ + +++ g l +p+nc+ el+
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78 pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517
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79
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80 LlkkcLnkDPskRpGsatakeilnhpwf<-*
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81 L++ c+ P++Rp ++ i h +
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82 pkinase_fu 518 LMRLCWSGHPTDRP---SFASI--HRIL 540
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83
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84 pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80
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85 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
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86 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
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87 pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
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88
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89 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
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90 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
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91 pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
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92
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93 ng........................gplsekeakkialQilrGleYLHs
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94 + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL +
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95 pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402
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96
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97 ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
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98 +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p +
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99 pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451
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100
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101 mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
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102 +m+PE ++++ y+s++DvW++Gv+L+E++++g
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103 pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483
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104
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105 dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
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106 ++P+++ + ee+ + +++ g l +p+nc+ el+
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107 pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517
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108
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109 LlkkcLnkDPskRpGsatakeil<-*
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110 L++ c+ P++Rp ++ i+
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111 pkinase_fu 518 LMRLCWSGHPTDRP---SFASIH 537
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112
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113 fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7
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114 CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.E
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115 *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq
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116 a ++++ + + ++W pp++ ++ + +++ Y v + +
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117 pkinase_fu 434 IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477
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118
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119 CS CCCCCC CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC
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120 pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
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121 + + + ++ + ++V+ +g+ S
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122 pkinase_fu 478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS 506
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123
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124 //
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125
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126 Query sequence: pkinase_part
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127 Accession: [none]
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128 Description: Dario rerio
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129
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130 Scores for sequence family classification (score includes all domains):
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131 Model Description Score E-value N
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132 -------- ----------- ----- ------- ---
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133 pkinase Protein kinase domain 101.5 1.7e-30 1
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134 pkinase Protein kinase domain -94.7 1.5e-05 1
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135 rrm -42.5 2.5 1
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136 rrm -8.7 3.7 1
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137 fn3 Fibronectin type III domain -9.0 3.8 1
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138 fn3 Fibronectin type III domain -52.2 5.9 1
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139
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140 Parsed for domains:
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141 Model Domain seq-f seq-t hmm-f hmm-t score E-value
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142 -------- ------- ----- ----- ----- ----- ----- -------
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143 rrm 1/1 169 180 .. 66 77 .] -8.7 3.7
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144 fn3 1/1 197 200 .. 81 84 .] -9.0 3.8
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145 fn3 1/1 233 299 .. 1 84 [] -52.2 5.9
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146 rrm 1/1 256 319 .. 1 77 [] -42.5 2.5
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147 pkinase 1/1 258 400 .] 1 116 [. 101.5 1.7e-30
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148 pkinase 1/1 258 400 .] 1 294 [] -94.7 1.5e-05
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149
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150 Alignments of top-scoring domains:
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151 rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
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152 *->nGkelggrklrv<-*
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153 n++ ++l v
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154 pkinase_pa 169 NKQDPHQHRLSV 180
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155
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156 fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
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157 CS CCCC
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158 *->GpeS<-*
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159 G eS
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160 pkinase_pa 197 GGES 200
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161
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162 fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9
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163 CS CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
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164 *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
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165 P + ++l ++ +s ls + p + i++ +R + ++g
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166 pkinase_pa 233 PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267
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167
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168 CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC
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169 neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
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170 g ++ gL P + ++ + + ++S
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171 pkinase_pa 268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS 299
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172
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173 rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
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174 *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
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175 +N++ +d+ e + F+ + +++ +
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176 pkinase_pa 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285
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177
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178 kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
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179 + V++ +ee+ ++ ++++ + l++ +
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180 pkinase_pa 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319
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181
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182 pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30
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183 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
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184 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
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185 pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
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186
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187 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
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188 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
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189 pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
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190
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191 ng........................gplsekeakkialQilrGleYL<-
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192 + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL
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193 pkinase_pa 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL 400
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194
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195 *
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196
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197 pkinase_pa - -
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198
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199 pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05
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200 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
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201 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
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202 pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
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203
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204 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
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205 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
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206 pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
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207
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208 nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi
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209 +
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210 pkinase_pa 353 RC------------------------------------------------ 354
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211
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212 aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL
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213 A++ s + +t++ ++ PE
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214 pkinase_pa 355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377
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215
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216 yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee
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217 +P s
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218 pkinase_pa 378 --------------------------------YPPLS------------- 382
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219
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220 lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp
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221 + + ++S+ + +
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222 pkinase_pa 383 -----CQ------EQLSISKQVAAGM-----------A------------ 398
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223
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224 wf<-*
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225 ++
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226 pkinase_pa 399 YL 400
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227
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228 //
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229
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230 Query sequence: S13421
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231 Accession: [none]
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232 Description: S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum.
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233
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234 Scores for sequence family classification (score includes all domains):
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235 Model Description Score E-value N
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236 -------- ----------- ----- ------- ---
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237 pkinase Protein kinase domain -171.6 0.19 1
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238 rrm -32.5 0.26 1
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239 rrm -6.1 0.92 1
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240 fn3 Fibronectin type III domain -39.7 1.2 1
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241 pkinase Protein kinase domain -9.2 1.8 1
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242 fn3 Fibronectin type III domain -7.5 1.9 1
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243
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244 Parsed for domains:
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245 Model Domain seq-f seq-t hmm-f hmm-t score E-value
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246 -------- ------- ----- ----- ----- ----- ----- -------
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247 fn3 1/1 143 224 .. 1 84 [] -39.7 1.2
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248 pkinase 1/1 233 241 .. 1 9 [. -9.2 1.8
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249 rrm 1/1 440 456 .. 1 17 [. -6.1 0.92
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250 rrm 1/1 669 731 .. 1 77 [] -32.5 0.26
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251 pkinase 1/1 906 1127 .. 1 294 [] -171.6 0.19
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252 fn3 1/1 923 934 .. 1 12 [. -7.5 1.9
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253
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254 Alignments of top-scoring domains:
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255 fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2
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256 CS C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
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257 *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
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258 + ++t+l++ dv ++ sWs+ +g+ + tg v R + ng +
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259 S13421 143 IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185
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260
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261 CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
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262 neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
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263 +++ ++ + + l L + + V v ++ +G
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264 S13421 186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH 224
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265
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266 pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8
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267 *->yelleklGe<-*
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268 +l+klGe
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269 S13421 233 VSTLKKLGE 241
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270
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271 rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92
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272 *->lfVgNLppdvteedLkd<-*
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273 + ++ L++ + d+ d
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274 S13421 440 VIISFLNEGLRQADIVD 456
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275
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276 rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26
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277 *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG
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278 V L+++d+ + + f i k++ D +
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279 S13421 669 --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699
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280
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281 faFVeFeseedAekAlealnGkelggr.klrv<-*
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282 + FV ++ + e+ ++ l k+++ +l++
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283 S13421 700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI 731
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284
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285 pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19
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286 *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes
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287 ++l G++ ++ + ++ ++ ++ + ++VAv + ++
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288 S13421 906 FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942
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289
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290 ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy
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291 + + L+ ++ fe + + v++ +d
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292 S13421 943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980
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293
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294 lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde
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295 l + +++ +s ++ Q+ lde
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296 S13421 981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007
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297
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298 ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l
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299 + ++ + LAr+l +++ + + +++++f+ +++ ++++l
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300 S13421 1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047
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301
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302 egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif
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303 +r s ++ W++++ vi+ ++ g
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304 S13421 1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073
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305
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306 vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL
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307 l++ +++ dp + + k l + ++++ ++l+ L +k++
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308 S13421 1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113
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309
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310 nkDPskRpGsatakeilnhpwf<-*
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311 +k +k p +i f
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312 S13421 1114 TKVFTKHP----DYQI----LF 1127
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313
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314 fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9
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315 CS CCCCCEEEEEEC
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316 *->PsaPtnltvtdv<-*
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317 + t+l++++v
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318 S13421 923 INPITGLSAREV 934
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319
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320 //
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321
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